Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks.

Copy number variations of colorectal cancer by whole exome sequencing data

Colorectal cancer (CRC) is the third most common cancer and the fourth leading cause of cancer death worldwide. About 85% of the cases of CRC are known to have chromosomal instability, an allelic imbalance at several chromosomal loci, and chromosome amplification and translocation. The aim of this study is to determine the recurrent copy number variant (CNV) regions present in stage II of CRC through whole exome sequencing, a rapidly developing targeted next-generation sequencing (NGS) technology that provides an accurate alternative approach for accessing genomic variations. 42 normal-tumor paired samples were sequenced by Illumina Genome Analyzer. Data was analyzed with Varscan2 and segmentation was performed with R package R-GADA. Summary of the segments across all samples was performed and the result was overlapped with DEG data of the same samples from a previous study in the group1. Major and more recurrent segments of CNV were: gain of chromosome 7pq(13%), 13q(31%) and 20q(75%) and loss of 8p(25%), 17p(23%), and 18pq(27%). This results are coincident with the known literature of CNV in CRC or other cancers, but our methodology should be validated by array comparative genomic hybridisation (aCGH) profiling, which is currently the gold standard for genetic diagnosis of CNV.

Variação anual de metilxantinas totais em amostras de Ilex paraguariensis A. St. - Hil. (erva-mate) em Ijuí e Santa Maria, Estado do Rio Grande do Sul

Ilex paraguariensis is a native plant in Southern Brazil, whose leaves are utilized in beverages such as chimarrão and tererê. This study investigated variations of total methylxanthines in leaves from two Ilex populations collected at one-month intervals over the course of one year. The levels varied from 1.92 to 10.37 mg/g (Ijuí) and 1.77 to 9.17 mg/g (Santa Maria). Statistical analysis indicated a significative variation in the contents of all samples analysed, confirming seasonal fluctuations. These results show that the period of harvest might decisively influence the organoleptic characteristics of raw material used in industry and therefore in commercial products.

Influência do método de extração nos teores de metilxantinas em erva-mate (Ilex paraguariensis a. St.-Hil., aquifoliaceae)

Ilex paraguariensis A. St. -Hil. is a native species of southern South America. The caffeine content in Ilex paraguariensis leaves has been considered an important quality parameter for maté-derived products. In this work different extraction methods for the determination of these methylxantines are compared. The influence of the extraction conditions on the methylxanthine yields was evaluated. Extraction by decoction with acidic aqueous solution (H2SO4 4N) presented the higher efficiency in the theobromine extraction. The extraction in a Soxhlet with acidic aqueous solution and decoction with acidic aqueous solution showed the highest caffeine yield. For the concomitant theobromine and caffeine quantification, the decoction with acidic aqueous solution is suggested.

Determinação do perfil de compostos voláteis e avaliação do sabor e aroma de bebidas produzidas a partir da erva-mate (Ilex paraguariensis)

Volatile compounds from green and roasted yerba mate were analyzed by gas chromatography/mass spectrometry and the flavor profile from yerba mate beverages was determined by descriptive quantitative analyses. The main compounds tentatively identified in green mate were linalool, alpha-terpineol and trans-linalool oxide and in roasted mate were (E,Z)-2,4-heptadienal isomers and 5-methylfurfural. Green mate infusion was qualified as having bitter taste and aroma as well as green grass aroma while roasted mate was defined as having a smooth, slightly burnt aroma. The relationship between the tentatively identified compounds and flavor must be determined by olfatometric analysis.

Determinação de compostos fenólicos por cromatografia líquida de alta eficiência isocrática durante estacionamento da erva-mate

Different phenolic compound, 5- caffeoylquinic acid (5-CQA), caffeic acid (AC) and rutin (Ru) contents of yerba-mate (Ilex paraguariensis) Brazilian samples of 06 different regions of São Mateus - Paraná, during natural and accelerated industrial storage, were evaluated. For quantification, a reverse phase HPLC isocratic method was developed and validated using methanol:water (35:65 v/v) acidified with 0.5% acetic acid as mobile phase and a photodiode array detector. The six sample global average contents were (34.90 and 36.10 mg g-1) for 5-CQA, (0.18 mg g-1 and 0.23 mg g-1) for AC and (7.12 and 7.18 mg g-1) for Ru, respectively, for the natural and accelerated storage systems. The results showed that the 5-CQA and Ru content are kept constant during the storage while AC content increase only during accelerated storage.

Foam-forming properties of Ilex paraguariensis (mate) saponin: foamability and foam lifetime analysis by Weibull equation

Saponins are natural soaplike foam-forming compounds widely used in foods, cosmetic and pharmaceutical preparations. In this work foamability and foam lifetime of foams obtained from Ilex paraguariensis unripe fruits were analyzed. Polysorbate 80 and sodium dodecyl sulfate were used as reference surfactants. Aiming a better data understanding a linearized 4-parameters Weibull function was proposed. The mate hydroethanolic extract (ME) and a mate saponin enriched fraction (MSF) afforded foamability and foam lifetime comparable to the synthetic surfactants. The linearization of the Weibull equation allowed the statistical comparison of foam decay curves, improving former mathematical approaches.

Ion pair-dispersive liquid-liquid microextraction of trace amount of rhodium ion in water and road dust samples prior to flame atomic absorption spectrometry determination

A simple ion pair-dispersive liquid-liquid microextraction method was proposed for preconcentration trace amounts of rhodium. An ion association complex of RhCl4- and tetradecyldimetylbenzylamonium was extracted into cholorobenzene. The volume and the type of extractive and dispersive solvents, the extraction time and the pH of the aqueous solutions were optimized. The calibration curve was linear in the range of 0.6-500 ng mL-1 of rhodium. The limit of detection was 0.10 ng mL-1 in initial solution and preconcentration factor was 40. The proposed method was successfully applied to the extraction and determination of rhodium in road dust and water samples.

Avaliação da labilidade de alumínio em infusões de erva-mate empregando voltametria adsortiva de redissolução catódica

Infusions of yerba mate obtained at different stages of industrialization were evaluated to determine the bioavailable fraction of Al. Adsorptive Cathodic Stripping Voltammetry using DASA (complexing agent) was applied to determine the labile fraction of Al at pH 5.0 and pH 8.0 for the total fraction of dissolved Al. The results indicate that on average 60% of Al is complexed with organic compounds, minimizing their bioavailability; however, the labile fraction exceeds by up to 4 times the maximum weekly intake recommended by the World Health Organization.

Real-time Musical Pair Improvisation on Mobile Devices

This thesis discusses the design and implementation of a real-time musical pair improvisation scenario for mobile devices. In the scenario transferring musical information over a network connection was required. The suitability of available wireless communication technologies was evaluated and communication was analyzed and designed on multiple layers of TCP/IP protocol stack. Also an application layer protocol was designed and implemented for the scenario. The implementation was integrated into a mobile musical software for children using available software components and libraries although the used platform lead to hardware and software constraints. Software limitations were taken into account in design. The results show that real-time musical improvisation can be implemented with wireless communication and mobile technology. The results also show that link layer had the most significant effect on real-time communication in the scenario.

Design and analysis of a transversal-flux switched-reluctance-linear-machine pole-pair

The Switched Reluctance technology is probably best suited for industrial low-speed or zerospeed applications where the power can be small but the torque or the force in linear movement cases might be relatively high. Because of its simple structure the SR-motor is an interesting alternative for low power applications where pneumatic or hydraulic linear drives are to be avoided. This study analyses the basic parts of an LSR-motor which are the two mover poles and one stator pole and which form the “basic pole pair” in linear-movement transversal-flux switchedreluctance motors. The static properties of the basic pole pair are modelled and the basic design rules are derived. The models developed are validated with experiments. A one-sided one-polepair transversal-flux switched-reluctance-linear-motor prototype is demonstrated and its static properties are measured. The modelling of the static properties is performed with FEM-calculations. Two-dimensional models are accurate enough to model the static key features for the basic dimensioning of LSRmotors. Three-dimensional models must be used in order to get the most accurate calculation results of the static traction force production. The developed dimensioning and modelling methods, which could be systematically validated by laboratory measurements, are the most significant contributions of this thesis.

Estudo comparativo de dellineamentos experimentais para estimativas de parâmetros genéticos em erva-mate (Ilex paraguariensis A. St. - Hil.)

O presente trabalho teve por objetivo comparar a eficiência do látice em relação aos delineamentos em blocos casualizados (DBC) e inteiramente casualizados (DIC) quanto aos caracteres altura e produção de massa verde em erva-mate (Ilex paraguariensis A. St. - Hil.). O experimento, conduzido na Fazenda Experimental do Canguiri, da Universidade Federal do Paraná, em Pinhais, PR, foi composto de cinco procedências, quatro com 13 e uma com 12 progênies de meias-irmãs. Cada progênie continha 54 plantas (nove parcelas de seis plantas). O experimento seguiu o modelo látice 8 x 8 com nove repetições balanceadas. As análises foram conduzidas usando-se tanto este modelo quanto os modelos DBC e DIC. Com relação ao caráter altura, a estimativa da eficiência do DBC em relação ao DIC (Êb/i) foi de 48,6%; do látice em relação ao DBC (Êl/b), de 61%; e do látice em relação ao DIC (Êl/i), de 139%. A estimativa da correlação intraclasse entre plantas dentro das parcelas (c²) foi de 9,4% para o DBC e zero para o látice. Para o caráter produção de massa verde, Êb/i, Êl/b e Êl/i foram de 14,3; 81,7; e 108%, respectivamente; e c², 16,9% para o DBC e 3,1% para o látice. Essas estimativas, associadas a uma estimativa de F de Snedecor altamente significativa dos dois caracteres, permitiram concluir que a capacidade de teste do DBC foi satisfatória para o caráter altura de plantas, mas insatisfatória para o caráter produção de massa verde.

Distribuição espacial e tamanho de amostra para o ácaro-do bronzeado da erva-mate

O ácaro Dichopelmus notus Keifer (Acari, Eriophyidae) provoca o bronzeamento e queda de folhas da erva-mate, reduzindo a produção e a qualidade de seus produtos. O acompanhamento dos níveis populacionais dessa espécie é importante para aprimorar seu manejo em plantios comerciais. Este trabalho teve por objetivos identificar a distribuição espacial e determinar o número de plantas e de folhas por planta que devem ser inspecionadas em cultivos comerciais de erva-mate em programas de monitoramento do ácaro-do-bronzeado. O estudo foi conduzido no Município de Chapecó, Santa Catarina, no período de janeiro de 2004 a janeiro de 2005. As avaliações foram realizadas quinzenalmente em um erval de 10 anos, dividido em três talhões com cerca de 2.500 m²cada, em que foram selecionadas 10 plantas ao acaso e em cada planta foi observado o número de ácaros em 18 folhas maduras. As inspeções foram executadas diretamente nos ervais com lentes com aumento de 10 vezes e 1 cm² de campo fixo. Constatou-se a distribuição espacial agregada para o ácaro, bem como a necessidade de inspecionar três folhas por planta, em 29 delas ao acaso e por hectare, de fevereiro a abril, para estimar a população com nível de precisão de 15%.

EFEITO DA ADIÇÃO DE RESÍDUOS DE PODA DA ERVA-MATE EM PAINÉIS AGLOMERADOS

O objetivo deste trabalho foi avaliar a viabilidade técnica da utilização de resíduos da poda de erva-mate na produção de painéis aglomerados. Foram produzidos painéis de aglomerados nas seguintes composições: 100% de pinus (T1), 100% de resíduos de erva-mate com casca (T2), 100% de resíduos de erva-mate sem casca (T3), 50% de pinus com 50% de resíduos de erva-mate com casca (T4) e 50% de pinus com 50% de resíduos de erva-mate sem casca (T5). Os painéis foram produzidos com o adesivo ureia-formaldeído a um teor de 8%, com ciclo de prensagem de 8 min, a 170 ºC e 30 kgf.cm-2. Os painéis produzidos com os resíduos de erva-mate apresentaram menor umidade de equilíbrio higroscópico (UEH), assim como menor absorção de água após 24 h de imersão (AA 24 h). Não houve diferença estatística entre os tratamentos quanto às propriedades de compressão, arrancamento de parafusos, dureza Janka e ligação interna. Os painéis produzidos com resíduos de erva-mate, assim como as misturas deles com partículas de pinus, apresentaram valores de módulo de ruptura à flexão estática inferiores aos estipulados pela norma brasileira NBR 14810-2 (ABNT, 2002). Como não atenderam a um dos requisitos mínimos, painéis produzidos com resíduos de erva-mate não devem ser utilizados em substituição aos painéis de madeira aglomerada.

Application of response surface methodology to study the biological removal of nitrogen from effluent of cattle slaughterhouse in a sequencing batch reactor

The aim of this study was to evaluate the efficiency of a sequencing batch reactor (SBR) on biological removal of nitrogen from cattle slaughterhouse wastewater by nitrification/denitrification processes. The effects of initial concentration of ammoniacal nitrogen were investigated at 100; 150 and 200 mg L-1 and air flow rate at 0.125; 0.375 and 0.625 L min¹ Lreactor-1 on the nitrogen compounds removal, by a Central Composite Rotational Design (CCRD) configuration. There were variations from 9.2 to 94.9%, 4.0 to 19.6% and 20.8 to 92.0% in the conversion of ammoniacal nitrogen to nitrate and nitrite concentration and removal of total nitrogen, respectively. The increase of air flow rate and decrease of the initial concentration of ammoniacal nitrogen resulted in higher efficiencies of total nitrogen removal, as well as the conversion of ammoniacal nitrogen to nitrate. During the pre-established intervals of this study, the removal and conversion efficiencies of nitrogen compounds above 85% were achieved in air flow rate variations from 0.375 to 0.725 L min-1 Lreactor-1 and initial concentration of ammoniacal nitrogen from 80 to 200 mg L-1. On denitrification process, we obtained efficiencies from 91.5 to 96.9% on the removal of nitrite/nitrate and from 78.3 to 87.9% on the removal of organic matter.